Package: crossmeta 1.33.1

Alex Pickering

crossmeta: Cross Platform Meta-Analysis of Microarray Data

Implements cross-platform and cross-species meta-analyses of Affymentrix, Illumina, and Agilent microarray data. This package automates common tasks such as downloading, normalizing, and annotating raw GEO data. The user then selects control and treatment samples in order to perform differential expression analyses for all comparisons. After analysing each contrast seperately, the user can select tissue sources for each contrast and specify any tissue sources that should be grouped for the subsequent meta-analyses.

Authors:Alex Pickering

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crossmeta.pdf |crossmeta.html✨
crossmeta/json (API)

# Install 'crossmeta' in R:
install.packages('crossmeta', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/alexvpickering/crossmeta/issues

Datasets:
  • gs.names - Map between KEGG pathway numbers and names.
  • gslist - KEGG human pathway genes.

On BioConductor:crossmeta-1.33.0(bioc 3.21)crossmeta-1.31.0(bioc 3.20)

geneexpressiontranscriptiondifferentialexpressionmicroarraytissuemicroarrayonechannelannotationbatcheffectpreprocessinggui

5.63 score 3 stars 19 scripts 266 downloads 25 exports 150 dependencies

Last updated 3 days agofrom:a60103dafe. Checks:OK: 1 ERROR: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 18 2024
R-4.5-winERRORDec 18 2024
R-4.5-linuxERRORDec 18 2024
R-4.4-winERRORDec 18 2024
R-4.4-macERRORDec 18 2024
R-4.3-winERRORDec 18 2024
R-4.3-macERRORDec 18 2024

Exports:add_adjustedadd_sourcesadd_vsdbulkPagebulkPageUIdiff_expres_metaexprs.MAfilter_genesfit_ebayesget_rawget_sva_modsget_top_tableget_vsdiqr_replicatesload_diffload_rawmakeExampleCountsEsetopen_raw_illumphenoData.ch2run_limmarun_limma_setuprun_svasetup_prevsymbol_annot

Dependencies:abindaffxparseraffyaffyioannotateAnnotationDbiaskpassbase64encBHBiobaseBiocGenericsBiocManagerBiocParallelBiostringsbitbit64bitopsblobbslibcachemcellrangerclicliprcodetoolscommonmarkcpp11crayoncrosstalkcurldata.tableDBIDelayedArraydigestdplyrDTedgeRevaluatefansifastmapfdrtoolfffontawesomeforeachformatRfsfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGEOquerygluehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2IRangesiteratorsjquerylibjsonliteKEGGRESTknitrlambda.rlaterlatticelazyevallifecyclelimmalocfitmagrittrMatrixMatrixGenericsmatrixStatsmemoisemetaMAmgcvmimeminiUINCmiscnlmeoligooligoClassesopensslpillarpkgconfigplogrpngpreprocessCoreprettyunitsprogresspromisespurrrR.methodsS3R.ooR.utilsR6rappdirsRcppRCurlreaderreadrreadxlrematchrentrezrlangrmarkdownRSQLitervestS4ArraysS4VectorssassselectrshinyshinyBSshinyjsshinypanelshinyWidgetsSMVarsnowsourcetoolsSparseArraystatmodstringistringrSummarizedExperimentsurvivalsvasystibbletidyrtidyselecttinytextzdbUCSC.utilsutf8vctrsvroomwithrxfunXMLxml2xtableXVectoryamlzlibbioc

Cross-Platform Meta Analysis

Alex Pickering

Rendered fromcrossmeta-vignette.Rmdusingknitr::rmarkdownon Dec 18 2024.

Last update: 2021-01-26
Started: 2016-09-28

Readme and manuals

Help Manual

Help pageTopics
Add expression data adjusted for pairs/surrogate variablesadd_adjusted
Add sample source information for meta-analysis.add_sources
Add VST normalized assay data element to expression setadd_vsd
Logic for Select Contrasts InterfacebulkPage
UI for Select Contrasts InterfacebulkPageUI
Differential expression analysis of esets.diff_expr
Effect size combination meta analysis.es_meta
Extract Log-Expression Matrix from MAListexprs.MA
Filter genes in RNA-seq ExpressionSetfilter_genes
Fit ebayes modelfit_ebayes
Attempts to fix Illumina raw data headerfix_illum_headers
Download and unpack microarray supplementary files from GEO.get_raw
Get model matrices for surrogate variable analysisget_sva_mods
Get top tableget_top_table
Get variance stabilized data for exploratory data analysisget_vsd
Map between KEGG pathway numbers and names.gs.names
KEGG human pathway genes.gslist
Count numeric columns in raw Illumina data filesilmn.nnum
Removes features with replicated annotation.iqr_replicates
Load Agilent raw dataload_agil_plat
Load previous differential expression analyses.load_diff
Load and annotate raw data downloaded from GEO.load_raw
Make example ExpressionSetmakeExampleCountsEset
Open raw Illumina microarray files.open_raw_illum
Construct AnnotatedDataFrame from Two-Channel ExpressionSetphenoData.ch2
Run prefix on Illumina raw data filesprefix_illum_headers
Remove columns that are autonamed by data.tableremove_autonamed
Linear model fitting of eset with limma.run_limma
Setup ExpressionSet for running limma analysisrun_limma_setup
Run surrogate variable analysisrun_sva
Setup selections when many samples.setup_prev
Add hgnc symbol to expression set.symbol_annot